Atomic force microscopy, a technique that has given us images of individual atoms and molecules, has racked up another success. A collaboration between the IBM-Zürich group (who have done so much in this area) and a group at the University of Santiago de Compostela (in Spain) has determined the structure of a reactive intermediate, and it’s not what one would have thought.
They’re working from a di-iodo derivative of the flat structures shown, and that turns into what can be variously drawn as a diradical (at top), an aryne (in the middle) or a cumulene (at bottom). You can change one into another by just moving electrons around, but the real species is probably a lot more like just one of them: but which one? This is not an easy question to answer by traditional physical organic chemistry, at least at this level of detail, but what if you could just reach down, pluck the iodines off a single molecule, and look at the result?
That’s the bizarre question that AFM lets you ask. The microscope tip (at high voltage) was used to break the iodo bonds, and then the isolated molecule was imaged (shown). Comparing bond lengths and angles, it looks a lot more like a cumulene than the other alternatives. It’s possible that being adsorbed onto a surface alters things as compared to a solution reaction, but under these conditions, a cumulene is apparently what you get.
And as that Chemistry World article says, this same technique can now be used for many other mechanistic questions. For those of us who grew up, scientifically, with mental pictures of fleeting reactive intermediates, things that could only be speculated on by watching the indirect evidence they leave behind. . .well, this is a bit spooky. But AFM images have always had that effect on me. Eventually, this will come to seem normal. And I wonder how far that will go? Can atomic force microscopy ever become a standard analytical technique – want to know a structure, just run the AFM tip over it? We’re a long way from that now (you’ll notice that the great majority of these sorts of papers come from just that IBM lab), but ruling out advances instrumentation is not the way to bet. I’m not expecting a walk-up instrument any time soon, but this looks like far too useful and powerful a technique to keep down for too long.